Required Packages (tested version)

• czifile (2019.7.2)
• pandas (1.3.4)
• numpy (1.21.4)
• pillow (8.4.0)
• tifffile (2021.11.2)

Export Channel Images in .tif or .png from CZI Format

Export channels from carl Zeiss image (.czi) formatted files. Needs a comma separated value (see test.csv) file to define the name for each channel. Also exports a list of generated fileprefixes (without channel subfix and file ending) as all.csv

How to run

This is the default configuration

CHANNEL_NAME = "ALL"
OUTPUT_TYPE = "TIF"

SLICE = 0

DATA_PATH = ""
CSV_FILE = "test.csv"
OUTPUT_PATH = "channels"

VERBOSE = False

Redefine at least CSV_FILE with a path to an appropriate .csv file. With the example test.csv file below run:

 python exportChannelsFromCZI.py

This will generate the following files:

channels/Image_DAPI.tif
channels/Image_Actin.tif
channels/Image2_DAPI.tif
channels/all.csv:

The all.csv list contains:

Image
Image2

Define Channel numbers and names (test.csv)

The file to define channel numbers and channel names must have the following (.csv) format:

folder,image,channel_nr,channel_name
folder1,Image.czi,0,DAPI
folder1,Image.czi,1,Actin
folder1,Image2.czu,0,DAPI